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Improving <i>in Silico</i>Prediction of Epitope Vaccine Candidates by Union and Intersection of Single Predictors

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World Journal of Vaccines 2011年第2期1卷 15-22页

作者： ivan Dimitrov Darren R. Flower Irini Doytchinova Life and Health Sciences Aston University United Kingdom School of Pharmacy Medical University of Sofia Bulgaria

the in silico prediction of peptide binding affinities to MHC proteins is a very important first step in the process of epi-tope-based vaccine design and development. Five MHC class II binding prediction servers were combined in different ways and the resulting performance of these combinations was evaluated using a test set, which consisted of 4540 known HLA-DRB1 binders. the five servers were: NetMHCIIpan, NetMHCII, ProPred, RANKPEP, and EpitOP. the top 5% of the ranked predictions from each server were combined using union and intersection operators. the outputs were evaluated in terms of sensitivity and positive predictive value (PPV). the union operator showed high sensitivity (65-79%) and low PPVs (6-8%), while intersection outputs had low sensitivities (4-41%) yet significantly higher PPVs (14-31%). thus there is a defining trade-off between sensitivity and PPV for each combination. the union of outputs from different servers brings more “noise” than “signal” to the resulting set of predicted binders. Conversely, selecting only commonly predicted binders increases the probability that an identified binder is a true binder.

关键词： MHC Class II Binders t-cell Epitopes HLA-DRB1 Alelles

A Versatile Phenotyping System and Analytics Platform Reveals Diverse temporal Responses to Water Availability in Setaria

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Molecular Plant 2015年第10期8卷 1520-1535页

作者： Noah Fahlgren Maximilian Feldman Malia A. Gehan Melinda S. Wilson Christine Shyu Douglas W. Bryant Steven t. Hill Colton J. McEntee ankalpi N. Warnasooriya Indrajit Kumar tracy Ficor Stephanie turnipseed Kerrigan B. Gilbert thomas P. Brutnell James C. Carrington todd C. Mockler ivan Baxter Donald Danforth Plant Science Center St. Louis MO 63132 USA USDA-ARS Donald Danforth Plant Science Center St. Louis MO 63132 USA these authors contributed equally to this article.

Phenotyping has become the rate-limiting step in using large-scale genomic data to understand and improve agricultural crops. Here, the Bellwether Phenotyping Platform for controlled-environment plant growth and automated multimodal phenotyping is described. the system has capacity for 1140 plants, which pass daily through stations to record fluorescence, near-infrared, and visible images. Plant Computer Vision （PlantCV） was developed as open-source, hardware platform-independent software for quantitative image analysis. In a 4-week experiment, wild Setaria viridis and domesticated Setaria italica had fundamentally different temporal responses to water availability. While both lines produced similar levels of biomass under limited water conditions, Setaria viridis maintained the same water-use efficiency under water replete conditions, while Setaria italica shifted to less efficient growth. Overall, the Bellwether Phenotyping Platform and PlantCV software detected significant effects of genotype and environment on height, biomass, water-use efficiency, color, plant architecture, and tissue water status traits. All -79 000 images acquired during the course of the experiment are publicly available.

关键词： abiotic/environmental stress water relations bioinformatics development phenotyping

Species diversity of Basidiomycota

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Fungal Diversity 2022年第3期114卷 281-325页

作者： Mao-Qiang He Rui-Lin Zhao Dong-Mei Liu teodor t.Denchev Dominik Begerow Andrey Yurkov Martin Kemler Ana M.Millanes Mats Wedin A.R.Mctaggart Roger G.Shivas Bart Buyck Jie Chen Alfredo Vizzini Viktor Papp ivan V.Zmitrovich Naveed Davoodian Kevin D.Hyde State Key Laboratory of Mycology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101People’s Republic of China College of Life Sciences University of Chinese Academy of SciencesHuairou DistrictBeijing 100408People’s Republic of China Institute of Ecology Chinese Reserach Academy of Environmental SciencesBeijing 100012People’s Republic of China Institute of Biodiversity and Ecosystem Research Bulgarian Academy of Sciences2 Gagarin St.1113 SofiaBulgaria Evolution der Pflanzen und Pilze Ruhr-Universität BochumND 03Universitätsstr.15044801 BochumGermany Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures Inhoffenstraße 7B38124 BraunschweigGermany Departamento de Biología y Geología Física y Química InorgánicaUniversidad Rey Juan Carlos28933 MóstolesSpain Department of Botany Swedish Museum of Natural HistoryP.O.Box 5000710405 StockholmSweden Queensland Alliance for Agriculture and Food Innovation The University of QueenslandBrisbane 4001Australia Centre for Crop Health University of Southern QueenslandToowoomba 4350Australia Institut pour Systematique EcologieBiodiversite(ISYEBUMR 7205)Sorbonne universitéMuséum National d’Histoire Naturelle CP 39CNRSDépartement Origines et Evolution12 Rue Buffon75005 ParisFrance Facultad de Ciencias Biológicas y Agropecuarias PeñuelaUniversidad VeracruzanaAmatlán de los Reyes94945 VeracruzMéxico Dipartimento di Scienze della Vita e Biologia dei Sistemi Universitàdi TorinoViale P.A.Mattioli 2510125 TorinoItaly Department of Botany Hungarian University of Agriculture and Life Sciences1518 BudapestHungary Komarov Botanical Institute Russian Academy of SciencesProfessor Popov st.2Saint PetersburgRussia 197376 Royal Botanic Gardens Victoria Birdwood AvenueMelbourneVIC 3004Australia Center of Excellence in Fungal Research Mae Fah Luang UniversityChiang Rai 57100Thailand CAS Key Laboratory for Plant Biodiversity and Biogeography of East Asia(KLPB) Kunming Institute of BotanyChinese Academy of Science

Fungi are eukaryotes that play essential roles in *** fungi,Basidiomycota is one of the major phyla with more than 40,000 described *** review species diversity of Basidiomycota from five groups with different lifestyles or habitats:saprobic in grass/forest litter,wood-decaying,yeast-like,ectomycorrhizal,and plant *** studies of Agaricus,Cantharellus,Ganoderma,Gyroporus,Russula,tricholoma,and groups of lichenicolous yeast-like fungi,rust fungi,and smut fungi are used to determine trends in discovery of *** each case study,the number of new species published during 2009–2020 is analysed to determine the rate of *** rates differ between taxa and reflect different states of progress for species discovery in different *** results showed that lichenicolous yeast-like taxa had the highest publication rate for new species in the past two decades,and it is likely this trend will continue in the next *** species discovery rate of plant parasitic basidiomycetes was low in the past ten years,and remained constant in the past 50 *** also found that the establishment of comprehensive and robust taxonomic systems based on a joint global initiative by mycologists could promote and standardize the recognition of *** estimated that more than 54,000 species of Basidiomycota will be discovered by 2030,and estimate a total of 1.4–4.2 million species of Basidiomycota *** numbers illustrate a huge gap between the described and yet unknown diversity in Basidiomycota.

关键词： Biodiversity Fungi Species number taxonomy

GStM1-null and GStt1-active genotypes as risk determinants of primary open angle glaucoma among smokers

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International Journal of Ophthalmology(English edition) 2018年第9期11卷 1514-1520页

作者： Miroslav Stamenkovic Vesna Lukic Sonja Suvakov tatjana Simic ivan Sencanic Marija Pljesa-Ercegovac Vesna Jaksic Sinisa Babovic Marija Matic Aleksandra Radosavljevic Ana Savic-Radojevic tatjana Djukic University Eye Clinic Medical Center ZvezdaraBelgrade 11000Serbia Faculty of Special Education and Rehabilitation University of BelgradeBelgrade 11000Serbia Institute of Medical and Clinical Biochemistry Belgrade 11000Serbia Faculty of Medicine University of BelgradeBelgrade 11000Serbia Hospital for Eye Diseases Clinical Center of SerbiaBelgrade 11000Serbia

AIM： to evaluate glutathione transferase theta 1 and mu 1（GStt1 and GStM1） polymorphisms as determinants of primary open angle glaucoma（POAG） risk, independently or in combination with cigarette smoking, hypertension and diabetes ***： A case-control study with 102 POAG patients and 202 age and gender-matched controls was carried out. Multiplex-polymerase chain reaction method was used for the analysis of GStM1 and GStt1 polymorphisms. the differences between two groups were tested by the t-test or χ~2 test. Logistic regression analysis was used for assessing the risk for disease ***： the presence of GStM1-null genotype did not contribute independently towards the risk of POAG. However, individuals with GStt1-active genotype were at almost two-fold increased risk to develop glaucoma（P=0.044） which increased up to 4.36 when combined with GStM1-null carriers（P=0.024）. When glutathione transferase（GSt） genotypes were analyzed in association with cigarette smoking, hypertension and diabetes, only carriers of GStt1-active genotype had significantly increased risk of POAG development in comparison with GStt1-null genotype individuals with no history of smoking, hypertension and diabetes, respectively （OR=3.52, P=0.003; OR=10.02, P〈0.001; OR=4.53, P=0.002）. CONCLUSION： the results obtained indicate that both GStM1-null and GStt1-active genotypes are associated with increased POAG risk among smokers, suggesting potential gene-environment interaction in glaucoma development.

关键词： GStM1 GStt1 primary open angle glaucoma risk smoking hypertension diabetes mellitus

Chemical Sensitivity of Luminescent Epitaxial Surface InP Quantum Dots

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Journal of Sensor technology 2013年第1期3卷 1-5页

作者： Roberta De Angelis Mauro Casalboni ivan Colantoni Liliana D’Amico Fabio De Matteis Fariba Hatami William t. Masselink Paolo Prosposito Department of Physics Humboldt University Berlin Germany INStM Research Unit of the University of Roma “Tor Vergata” Rome Italy Physics Department University of Rome “Tor Vergata” Rome Ital Physics Department University of Rome “Tor Vergata” Rome Italy

Surface InP quantum dots grown by gas source molecular beam epitaxy on In0.48Ga0.52P buffer layer lattice matched to GaAs substrate shows a broad-band near-infrared photoluminescence ranging from 750 to 865 nm dependent on their dimensions. A reversible luminescence intensity enhancement has been observed when the quantum dots were exposed to vapours of different chemical solvents with the highest sensitivity for alcohol (methanol and ethanol) vapours. the luminescent behaviour is dependent on the solvent type and concentration. the peak energy and band shape of the luminescence are not affected by the solvent vapour.

关键词： Vapour Sensitivity Quantum Dot Photoluminescence InP Organic Solvent

A review of particulate-reinforced aluminum matrix composites fabricated by selective laser melting

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transactions of Nonferrous Metals Society of China 2020年第8期30卷 2001-2034页

作者： Pei WANG Jürgen ECKERt Konda-gokuldoss PRASHANtH Ming-wei WU ivan KABAN Li-xia XI Sergio SCUDINO Additive Manufacturing Institute Shenzhen UniversityShenzhen 518060China Institute for Complex Materials IFW DresdenD-01069 DresdenGermany Erich Schmid Institute of Materials Science Austrian Academy of SciencesA-8700 LeobenAustria Department of Materials Science Montanuniversität LeobenA-8700 LeobenAustria Department of Mechanical and Industrial Engineering Tallinn University of Technology19086 TallinnEstonia CBCMt School of Mechanical EngineeringVellore Institute of TechnologyVellore-632014Tamil NaduIndia Department of Materials and Mineral Resources Engineering Taipei University of TechnologyTaipei 10608China College of Materials Science and technology Nanjing University of Aeronautics and AstronauticsNanjing 210016China

Selective laser melting(SLM)is an emerging layer-wise additive manufacturing technique that can generate complex components with high ***-reinforced aluminum matrix composites(PAMCs)are important materials for various applications due to the combined properties of Al matrix and *** the advantages of SLM technology and PAMCs,the novel SLM PAMCs have been developed and researched in recent ***,the current research progress about the SLM PAMCs is ***,special attention is paid to the solidification behavior of SLM ***,the important issues about the design and fabrication of high-performance SLM PAMCs,including the selection of reinforcement,the influence of parameters on the processing and microstructure,the defect evolution and phase control,are highlighted and discussed ***,the performance and strengthening mechanism of SLM PAMCs are systematically figured ***,future directions are pointed out on the advancement of high-performance SLM PAMCs.

关键词： selective laser melting aluminum matrix composites solidification behavior microstructure properties

Efficient IL-2R signaling differentially affects the stability,function,and composition of the regulatory t-cell pool

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Cellular & Molecular Immunology 2021年第2期18卷 398-414页

作者： Marc Permanyer Berislav Bošnjak Silke Glage Michaela Friedrichsen Stefan Floess Jochen Huehn Gwendolyn E.Patzer ivan Odak Nadine Eckert Razieh Zargari Laura Ospina-Quintero Hristo Georgiev Reinhold Förster Institute of Immunology Hannover Medical SchoolHannoverGermany Institute for Laboratory Animal Science Hannover Medical SchoolHannoverGermany Department Experimental Immunology Helmholtz Centre for Infection ResearchBraunschweigGermany Cluster of Excellence RESISt(EXC 2155) Hannover Medical School30625HannoverGermany

Signaling via interleukin-2 receptor(IL-2R)is a requisite for regulatory t(treg)cell identity and ***,it is not completely understood to what degree IL-2R signaling is required for treg cell homeostasis,lineage stability and function in both resting and inflammatory ***,we characterized a spontaneous mutant mouse strain endowed with a hypomorphic tyr129His variant of CD25,theα-chain of IL-2R,which resulted in diminished receptor expression and reduced IL-2R *** noninflammatory conditions,Cd25Y129H mice harbored substantially lower numbers of peripheral treg cells with stable Foxp3 expression that prevented the development of spontaneous autoimmune *** contrast,Cd25^(Y^(129H))treg cells failed to efficiently induce immune suppression and lost lineage commitment in a t-cell transfer colitis model,indicating that unimpaired IL-2R signaling is critical for treg cell function in inflammatory ***,single-cell RNA sequencing of treg cells revealed that impaired IL-2R signaling profoundly affected the balance of central and effector treg cell ***,partial loss of IL-2R signaling differentially interferes with the maintenance,heterogeneity,and suppressive function of the treg cell pool.

关键词： Regulatory t cells IL-2R signaling scRNA sequencing treg heterogeneity

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热处理低温钠长石的EPR和X射线衍射研究

矿物学报 1989年第4期9卷 296-303页

作者：富毓德 ivan Petrov S.S.Hafner 中国科学院地球化学研究所联邦德国马尔堡大学矿物与结晶学研究所

利用电子顺磁共振(EPR)和X射线衍射方法研究了天然和热处理钠长石单晶。热处理在500—850℃水热条件下完成。在外加磁场B平行于晶体c~*轴的方向上,测量了加热前后Fe^(3+)的EPR谱和线宽△B随温度和加热时间的变化。结果显示,线宽随Al、S... 详细信息

利用电子顺磁共振(EPR)和X射线衍射方法研究了天然和热处理钠长石单晶。热处理在500—850℃水热条件下完成。在外加磁场B平行于晶体c~*轴的方向上,测量了加热前后Fe^(3+)的EPR谱和线宽△B随温度和加热时间的变化。结果显示,线宽随Al、Si无序的增大而增加。由此得出结论,在低温钠长石中,Fe^(3+)位于Al^(3+)占据的t_1(o)位置,在被研究的温度范围内,Fe^(3+)未参与四面体位置t间Al、Si交换。谱线的加宽主要是由在Fe^(3+)邻近位置上Al、Si无序的增大引起的,同时与观测到的晶胞参数变化有关。在Al、Si无序更强的晶体中,Fe^(3+)谱变得极宽。

关键词：钠长石矿物热处理 EPR X射线衍射

碱性长石中Fe^(3+)在四面体位置间交换动力学的EPR研究

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矿物学报 1989年第2期9卷 97-103页

作者：富毓德 ivan Petrov S.S.Hafner 中国科学院地球化学研究所联邦德国马尔堡大学矿物学与结晶学研究所

在加热条件下,利用EPR方法研究了碱性长石中不同四面体位置间的Fe^(3+)、Al^(3+)交换。低温钠长石和透长石晶体分别在水热,1 kbar,500—900℃和干加热,1050℃条件下加热。在低温钠长石中,加热后Fe^(3+)线被加宽,当温度为800℃时,除t_1(o... 详细信息

在加热条件下,利用EPR方法研究了碱性长石中不同四面体位置间的Fe^(3+)、Al^(3+)交换。低温钠长石和透长石晶体分别在水热,1 kbar,500—900℃和干加热,1050℃条件下加热。在低温钠长石中,加热后Fe^(3+)线被加宽,当温度为800℃时,除t_1(o)位置外,没有出现其余四面体位置Fe^(3+)产生的谱线。透长石在1050℃加热1300h后,t_1和t_2线的相对强度发生了变化。实验表明,在碱性长石中不同四面体间Fe^(3+)、Ak^(3+)和Fe^(3+)、Si^(4+)交换与Al^(3+)、Si^(4+)交换比较,前者速度要缓慢得多。

关键词：长石碱性 Fe^3+ 动力学 EPR法